Black Spots and Corruption During Mesh Edit
All right I don't know. I guess the problem bred from the software I used to extract the model (Ninjaripper). It created a weird data layer of normals information (sharp-edge, smooth-face, etc) which doesn't show up in the viewport edit. It makes precious little sense to me, and the man-pages aren't very clear on the subject at all.

The fix as I mentioned above is to remove the data layer before editing, then replace it again afterwards.

Run it up the flagpole...